diff --git a/workflows/virology/pox-virus-amplicon/CHANGELOG.md b/workflows/virology/pox-virus-amplicon/CHANGELOG.md index aaa34b3cea..b958219d7a 100644 --- a/workflows/virology/pox-virus-amplicon/CHANGELOG.md +++ b/workflows/virology/pox-virus-amplicon/CHANGELOG.md @@ -1,5 +1,17 @@ # Changelog +## [0.3] 2025-02-10 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4` +- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2` +- `toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0` + ## [0.2] 2024-06-19 ### Tool version updates diff --git a/workflows/virology/pox-virus-amplicon/pox-virus-half-genome.ga b/workflows/virology/pox-virus-amplicon/pox-virus-half-genome.ga index fe2d9fcb74..1ac6b8b29a 100644 --- a/workflows/virology/pox-virus-amplicon/pox-virus-half-genome.ga +++ b/workflows/virology/pox-virus-amplicon/pox-virus-half-genome.ga @@ -16,7 +16,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2", + "release": "0.3", "name": "Pox Virus Illumina Amplicon Workflow from half-genomes", "steps": { "0": { @@ -210,7 +210,7 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", "errors": null, "id": 7, "input_connections": { @@ -244,15 +244,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", "tool_shed_repository": { - "changeset_revision": "7d37cfda8e00", + "changeset_revision": "5cbde03c1103", "name": "fasta_compute_length", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"ref\": {\"ref_source\": \"history\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"keep_first_word\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.3", + "tool_version": "1.0.4", "type": "tool", "uuid": "f562eb06-797e-4efb-a464-6d368f573dbe", "when": null, @@ -399,7 +399,7 @@ }, "11": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4", "errors": null, "id": 11, "input_connections": { @@ -464,15 +464,15 @@ "output_name": "report_html" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4", "tool_shed_repository": { - "changeset_revision": "c59d48774d03", + "changeset_revision": "10678d49d39e", "name": "fastp", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.23.4+galaxy0", + "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 1, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"merge_reads\": {\"merge\": \"\", \"__current_case__\": 1}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\", \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.24.0+galaxy4", "type": "tool", "uuid": "bf2dc639-b721-4ca5-a1a3-0a55d1185143", "when": null, @@ -879,7 +879,7 @@ }, "21": { "annotation": "", - 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"changeset_revision": "ce385837c160", + "changeset_revision": "63dd26468588", "name": "emboss_5", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1254,7 +1254,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0", "tool_shed_repository": { - "changeset_revision": "ce385837c160", + "changeset_revision": "63dd26468588", "name": "emboss_5", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1414,7 +1414,7 @@ }, "30": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 30, "input_connections": { @@ -1445,15 +1445,15 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"quality\": \"20\", \"library\": \"\", \"cigarcons\": null, \"inclusive_filter\": [\"1\", \"2\"], \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": \"\", \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"fraction\", \"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": null}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": \"20\", \"library\": \"\", \"cigarcons\": null, \"inclusive_filter\": [\"1\", \"2\"], \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": \"\", \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"fraction\", \"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": null}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "16002ad4-640a-4e3c-bf60-dbcb05de92ae", "when": null, @@ -1500,7 +1500,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "tool_shed_repository": { - "changeset_revision": "fed4aa48ba09", + "changeset_revision": "541082d03bef", "name": "samtools_stats", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1520,7 +1520,7 @@ }, "32": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 32, "input_connections": { @@ -1551,15 +1551,15 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"quality\": \"20\", \"library\": \"\", \"cigarcons\": null, \"inclusive_filter\": [\"1\", \"2\"], \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": \"\", \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"fraction\", \"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": null}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": \"20\", \"library\": \"\", \"cigarcons\": null, \"inclusive_filter\": [\"1\", \"2\"], \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": \"\", \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"fraction\", \"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": null}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "229c546c-d0bb-4152-b01a-719085f0e830", "when": null, @@ -1606,7 +1606,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "tool_shed_repository": { - 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